Motivation
The alignment of biological sequences obtained from an
algorithm will in general contain both correct and wrong
parts. Hence, to allow for a valid interpretation of the
alignment, the local trustworthiness of the alignment has to
be quantified.

Results
We present a novel approach that attributes a reliability
index to every pair, including gapped regions, in the optimal
alignment of two protein sequences. The method is based on a
fuzzy recast of the dynamic programming algorithm for
sequence alignment in terms of mean field annealing. An
extensive evaluation with structural reference alignments not
only shows that the probability for a pair to be correctly
aligned grows consistently with increasing reliability index,
but moreover demonstrates that the value of the reliability
index can directly be translated into an estimate of the
probability for a correct alignment.